Trade-Offs Between Reducing Complex Terminology and Producing Accurate Interpretations from Environmental DNA: Comment on “Environmental DNA: What\u27s behind the term?” by Pawlowski et al., (2020)

In a recent paper, “Environmental DNA: What\u27s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spatiotemporal variation in mammal eDNA signals. We hypothesised eDNA signals would be stronger for semi-aquatic than terrestrial mammals, and at sites where individuals exhibited behaviours. In captivity, we sampled waterbodies at points where behaviours were observed (‘directed’ sampling) and at equidistant intervals along the shoreline (‘stratified’ sampling). We surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers. All focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between semi-aquatic or terrestrial species, or according to behaviours. eDNA was evenly distributed in artificial waterbodies, but unevenly distributed in natural ponds. Survey methods deployed at natural ponds shared three species detections. Metabarcoding missed badger and red fox recorded by cameras and field signs, but detected small mammals these tools overlooked, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected less frequently than semi-aquatic mammal eDNA signals. eDNA metabarcoding could enhance mammal monitoring through large-scale, multi-species distribution assessment for priority and difficult to survey species, and provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before routine implementation

Effective monitoring of freshwater fish

Freshwater ecosystems constitute only a small fraction of the planet’s water resources, yet support much of its diversity, with freshwater fish accounting for more species than birds, mammals, amphibians, or reptiles. Fresh waters are, however, particularly vulnerable to anthropogenic impacts, including habitat loss, climate and land use change, nutrient enrichment, and biological invasions. This environmental degradation, combined with unprecedented rates of biodiversity change, highlights the importance of robust and replicable programmes to monitor freshwater fish assemblages. Such monitoring programmes can have diverse aims, including confirming the presence of a single species (e.g. early detection of alien species), tracking changes in the abundance of threatened species, or documenting long-term temporal changes in entire communities. Irrespective of their motivation, monitoring programmes are only fit for purpose if they have clearly articulated aims and collect data that can meet those aims. This review, therefore, highlights the importance of identifying the key aims in monitoring programmes, and outlines the different methods of sampling freshwater fish that can be used to meet these aims. We emphasise that investigators must address issues around sampling design, statistical power, species’ detectability, taxonomy, and ethics in their monitoring programmes. Additionally, programmes must ensure that high-quality monitoring data are properly curated and deposited in repositories that will endure. Through fostering improved practice in freshwater fish monitoring, this review aims to help programmes improve understanding of the processes that shape the Earth's freshwater ecosystems, and help protect these systems in face of rapid environmental change

Characterization of Hydropsyche slossonae (Trichoptera : Hydropsychidae) capture net polypeptides

The aim of this study was to characterize polypeptide components of the capture net spun by trichopteran larvae Hydropsyche slossonae (Banks) (Trichoptera: Hydropsychidae). Thirty-one polypeptide bands were identified by SDS - polyacrylamide gel electrophoresis (SDS-PAGE) from extracted net material, with molecular weights ranging from 8500 to 179 000. Comparison with published data on Bombyx mori (L.) (Lepidoptera: Bombycidae) silk, treated under similar denaturing conditions, shows that six low molecular weight polypeptides ranging between 8500 and 18 800 in the silk of H. slossonae are absent from that of B. mori; furthermore, two high molecular weight polypeptides (210 000 and 220 000) detected in the silk of B. mori are not present in that of H. slossonae. Differences between both groups are probably related to their mode of living and to the specific use of silk (in air versus under water). Our findings are consistent with the current trend in the literature that silk spun by aquatic and terrestrial insects, as well as those spun by different species, is apparently made of different biopolymers according to the protein constituents. Hence, the polypeptide characterization of silk, combined with sequence data and (or) antibodies cross-reactivity data, could represent a potential tool for taxonomic classification improvement of aquatic insects. These results could eventually be used to characterize hydropsychid capture net anomalies induced by environmental pollution

Anomalies on capture nets of Hydropsyche slossonae larvae (Trichoptera; Hydropsychidae) following a sublethal chronic exposure to cadmium

A laboratory study on the sublethal effects of cadmium (Cd) on the net-spinning process of the larvae of Hydropsyche slossonae was conducted in order to assess the potential of net anomalies as an indicator of chronic exposure to Cd. Two major anomalies with different frequency levels were identified after chronic exposure to 0.37, 1.2, 11.6, 21.4 and 43.3 μg l−1 of Cd. The first was a distortion of the midline meshes where the diamond-shape structure is disrupted and the meshes are separated by extra strands (called ‘midline’ anomaly). The second aberration consisted of a distortion of the rectilinear structure of net opening by strands being fused or added over the meshes (called ‘crossover’ anomaly). The midline distortion may be linked to a physiological stress caused by Cd, which can affect the control of the net-spinning process. It was not possible to relate the crossover aberrations to a specific toxic action of Cd, but data indicated that both anomalies are independent from each other and that two modes of action could be implicated. Protein analyses of capture nets have revealed silk polypeptide modifications at the highest Cd concentration tested, indicating a possible effect of Cd interaction with silk proteins. However, neither a gradient-concentration nor a time-dependent response could be established with both aberration frequencies. Silk protein modifications would rather play a secondary role in the appearance of both net anomalies, and mostly at a high concentration level. Finally, the toxicity curves (EC50) show that the sensitivity threshold for both types of aberration ranged from 1 to 5 μg l−1 which is highly sensitive compared with other sublethal effects of Cd on other macroinvertebrate species. Hence, the use of capture-net anomalies of hydropsychid larvae would represent a valuable indicator of sublethal toxicity induced by Cd and possibly by other metals in running waters

Anomalies on capture nets of Hydropsyche slossonae larvae (Trichoptera; Hydropsychidae), a potential indicator of chronic toxicity of malathion (organophosphate insecticide)

A laboratory study on the sublethal effects of malathion on the net-spinning behavior of the caddisfly larvae Hydropsyche slossonae was conducted in order to assess the potential of net anomalies as an indicator of chronic exposure to organophosphorus insecticides. Two anomalies were identified after chronic exposure to 0.01, 0.05, 0.1, 0.5 and 1.0 μg l−1 malathion. The first was a distortion of the midline meshes where the normal diamond shape structure was disrupted and the meshes were separated by extra strands (called ‘midline’ anomaly). The second aberration observed was a significant decrease in net symmetry. Both anomalies were highly correlated to the toxic action of malathion, i.e. inhibition of the acetylcholinesterase enzyme (AChE). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses of capture nets did not show any modification of silk polypeptides after exposure to malathion, indicating that net distortions were not related to silk composition. Both anomalies seem to represent the symptoms of the specific toxic action of malathion; nevertheless, they can serve as an index of the physiological condition of the larvae, especially the midline anomaly. The symmetry of the nets decreased significantly after exposure to 0.5 and 1.0 μg l−1. However, the toxicity curves (EC50) showed that the sensitivity threshold for the midline anomaly ranged from 0.11 to 0.28 μg l−1, which reflect more realistic exposure to concentrations expected to occur in the field. Hence, the use of capture net anomalies of hydropsychid larvae could represent a valuable indicator of sublethal toxicity induced by malathion and other organophosphorus insecticides in running waters